Functional metatranscriptomics of the rhizosphere: towards an understanding of metabolic processes of the microbial carbon pump.

The soil microbiome drives soil organic carbon (SOC) transformation, shaped and impacted by plant growth stage and soil management such as tillage. The soil microbial carbon pump conceptually links the degradation of plant- and microbe-derived compounds and the neosynthesis of microbial biomass, as a driver of SOC buildup. Using metatranscriptomic sequencing, we characterized actively expressed microbial functions associated with the microbial carbon pump in the Brassica napus rhizosphere across growth stages and under simulated erosion, using a tailored KEGG Orthology (KO) approach complemented by CAZy analysis of carbohydrate-active enzyme transcripts. A clear growth stage effect emerged with higher transcript abundances at flowering. Transcripts for substrate-binding proteins and permeases of ABC transporters (e.g. xylose, trehalose, phospholipids) increased at flowering, while plant polymer-degrading transcripts remained unaffected. Elevated transcripts for chitin synthase, glmS (peptidoglycan precursor), and EPS-related genes (ExoY, algF, cysE) at flowering suggested enhanced microbial activity. Simulated soil erosion impacted only two KO transcripts. CAZy results showed the same pattern with GH related to sugars and plant polymers increased at flowering. Despite functional shifts, taxonomic composition stayed stable for most affected transcripts. Our study uncovered metabolic pathways associated with SOC transformation and microbe-derived SOC neosynthesis, offering insights into microbial contributions to SOC formation and persistence.